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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.11

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2022-06-15, 20:43 based on data in: /home/chengxin/pmultiqctest/test_dia/results


        pmultiqc

        pmultiqc is an module to show the pipeline performance.

        Experimental Design

        This plot shows the Proteomics Experimental Design

        This plot shows the Proteomics Experimental Design. You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html

        Showing 4/4 rows and 6/6 columns.
        Spectra FileFraction_GroupFractionLabelSampleMSstats_ConditionMSstats_BioReplicate
        RD139_Narrow_UPS1_0_1fmol_inj1.mzML1111
        CT=Mixture;CN=UPS1;QY=0.1fmol
        1
        RD139_Narrow_UPS1_0_1fmol_inj2.mzML2111
        CT=Mixture;CN=UPS1;QY=0.1fmol
        1
        RD139_Narrow_UPS1_0_25fmol_inj1.mzML3112
        CT=Mixture;CN=UPS1;QY=0.25fmol
        2
        RD139_Narrow_UPS1_0_25fmol_inj2.mzML4112
        CT=Mixture;CN=UPS1;QY=0.25fmol
        2

        Summary Table

        This plot shows the quantms pipeline summary statistics

        This plot shows the quantms pipeline summary statistics

        Showing 1/1 rows and 2/2 columns.
        Total MS/MS SpectralTotal Peptide QuantifiedTotal Protein Quantified
        573300
        5729
        1605

        Pipeline Result Statistics

        This plot shows the quantms pipeline final result

        This plot shows the quantms pipeline final result. Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、 and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.

        Showing 4/4 rows and 7/7 columns.
        Spectra FileSample Nameconditionfractionpeptide_numunique_peptide_nummodified_peptide_numprotein_num
        RD139_Narrow_UPS1_0_1fmol_inj1.mzML
        1
        CT=Mixture;CN=UPS1;QY=0.1fmol
        1
        5407
        5407
        871
        1552
        RD139_Narrow_UPS1_0_1fmol_inj2.mzML
        1
        CT=Mixture;CN=UPS1;QY=0.1fmol
        1
        5434
        5434
        880
        1562
        RD139_Narrow_UPS1_0_25fmol_inj1.mzML
        2
        CT=Mixture;CN=UPS1;QY=0.25fmol
        1
        5572
        5572
        901
        1578
        RD139_Narrow_UPS1_0_25fmol_inj2.mzML
        2
        CT=Mixture;CN=UPS1;QY=0.25fmol
        1
        5558
        5558
        896
        1588

        Number of Peptides Per Protein

        This plot shows the number of peptides per proteins in quantms pipeline final result

        This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.

        loading..

        Distribution of precursor charges

        This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.

        This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.

        loading..

        Number of Peaks per MS/MS spectrum

        This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).

        loading..

        Peak Intensity Distribution

        This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.

        Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.

        loading..

        Peptides Quantification Table

        This plot shows the quantification information of peptidesin quantms pipeline final result

        The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.

        • BestSearchScore: It is equal to 1 - min(Q.Value) for DIA datasets. Then it is equal to 1 - min(best_search_engine_score[1]), which is from best_search_engine_score[1] column in mzTab peptide table for DDA datasets.
        • Average Intensity: Average intensity of each peptide sequence across all conditions with NA=0 or NA ignored.
        • Peptide intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of fractions, and then mean intensity in technical replicates/biological replicates separately. Click distribution to switch to bar plots.
        Showing 50/50 rows and 8/8 columns.
        indexProteinNamePeptideSequenceBestSearchScoreAverage IntensityCT=Mixture;CN=UPS1;QY=0.25fmolCT=Mixture;CN=UPS1;QY=0.1fmolCT=Mixture;CN=UPS1;QY=0.25fmolCT=Mixture;CN=UPS1;QY=0.1fmol
        1
        TOLA_ECOLI
        AAAEADDIFGELSSGK
        1.00000
        5.926
        5.96355
        5.88893
        2
        G3P2_ECOLI
        AAAENIIPHTTGAAK
        0.99999
        6.126
        6.16983
        6.08148
        3
        RLMH_ECOLI
        AAAEQSWSLSALTLPHPLVR
        0.99998
        6.237
        6.27871
        6.19528
        4
        PDXJ_ECOLI
        AAAEVGAPFIEIHTGC(Carbamidomethyl)YADAK
        0.99966
        5.387
        5.27598
        5.49758
        5
        RL10_ECOLI
        AAAFEGELIPASQIDR
        1.00000
        8.548
        8.59019
        8.50557
        6
        YFGM_ECOLI
        AAAQLQQGLADTSDENLK
        1.00000
        6.689
        6.67992
        6.69790
        7
        YFGM_ECOLI
        AAAQLQQGLADTSDENLKAVINLR
        1.00000
        6.154
        6.27640
        6.03208
        8
        RHLE_ECOLI
        AAATGEALSLVC(Carbamidomethyl)VDEHK
        0.99998
        5.706
        5.73314
        5.67986
        9
        SYP_ECOLI
        AAATQEMTLVDTPNAK
        1.00000
        6.278
        6.35184
        6.20352
        10
        EUTL_ECOLI
        AAC(Carbamidomethyl)NAFTDAVLEIAR
        1.00000
        5.629
        5.65410
        5.60437
        11
        ACRB_ECOLI
        AADGQMVPFSAFSSSR
        0.99998
        6.060
        6.18081
        5.93873
        12
        YIDA_ECOLI
        AADGSTVAQTALSYDDYR
        0.99984
        5.699
        5.71442
        5.68264
        13
        ADHE_ECOLI
        AADIVLQAAIAAGAPK
        1.00000
        7.676
        7.70587
        7.64709
        14
        NARG_ECOLI
        AADLVDALGQENNPEWK
        1.00000
        5.691
        5.73571
        5.64536
        15
        DNAK_ECOLI
        AADNKSLGQFNLDGINPAPR
        0.99984
        5.523
        5.55101
        5.49575
        16
        OXYR_ECOLI
        AADSC(Carbamidomethyl)HVSQPTLSGQIR
        1.00000
        6.582
        6.61358
        6.54958
        17
        TALA_ECOLI
        AAEELEKEGINC(Carbamidomethyl)NLTLLFSFAQAR
        1.00000
        6.261
        6.31525
        6.20589
        18
        HEMY_ECOLI
        AAELAGNDTIPVEITR
        0.99995
        6.439
        6.45229
        6.42564
        19
        SYL_ECOLI
        AAENNPELAAFIDEC(Carbamidomethyl)R
        1.00000
        6.983
        7.02417
        6.94120
        20
        TALB_ECOLI
        AAEQLEKEGINC(Carbamidomethyl)NLTLLFSFAQAR
        1.00000
        6.974
        7.05119
        6.89627
        21
        MBHM_ECOLI
        AAESALNIDVPVNAQYIR
        1.00000
        6.134
        6.13665
        6.13039
        22
        DNAG_ECOLI
        AAESGVSRPVPQLKR
        0.99994
        5.094
        5.22879
        4.95849
        23
        HDFR_ECOLI
        AAESLYLTQSAVSFR
        1.00000
        6.053
        6.09457
        6.01157
        24
        RNE_ECOLI
        AAESRPAPFLIHQESNVIVR
        1.00000
        6.575
        6.59255
        6.55722
        25
        HFLK_ECOLI
        AAFDDAIAARENEQQYIR
        1.00000
        5.778
        5.92097
        5.63543
        26
        AROF_ECOLI
        AAFPLSLQQEAQIADSR
        1.00000
        5.927
        5.92407
        5.93057
        27
        AROF_ECOLI
        AAFPLSLQQEAQIADSRK
        0.99984
        5.760
        5.78874
        5.73177
        28
        BOLA_ECOLI
        AAFQPVFLEVVDESYR
        1.00000
        6.729
        6.74543
        6.71178
        29
        CLPB_ECOLI
        AAGATTANITQAIEQMR
        1.00000
        6.070
        6.16686
        5.97263
        30
        YBIS_ECOLI
        AAGEPLPAVVPAGPDNPMGLYALYIGR
        1.00000
        5.949
        6.05959
        5.83808
        31
        SDHA_ECOLI
        AAGLHLQESIAEQGALR
        1.00000
        5.422
        5.41540
        5.42948
        32
        TALA_ECOLI
        AAGLSQYEHLIDDAIAWGK
        0.99984
        5.179
        5.24132
        5.11623
        33
        TALA_ECOLI
        AAGLSQYEHLIDDAIAWGKK
        1.00000
        5.820
        5.86380
        5.77630
        34
        ADHE_ECOLI
        AAGVETEVFFEVEADPTLSIVR
        0.99999
        6.465
        6.41371
        6.51683
        35
        ADHE_ECOLI
        AAGVETEVFFEVEADPTLSIVRK
        0.99984
        6.829
        6.88191
        6.77579
        36
        ENO_ECOLI
        AAGYELGKDITLAMDC(Carbamidomethyl)AASEFYK
        1.00000
        6.646
        6.66359
        6.62909
        37
        YEBE_ECOLI
        AAHQDEPQFGAQSTPLDER
        0.99984
        5.648
        5.67456
        5.62198
        38
        RIBB_ECOLI
        AAIADGAKPSDLNRPGHVFPLR
        1.00000
        6.462
        6.49256
        6.43130
        39
        DEOC_ECOLI
        AAIAYGADEVDVVFPYR
        1.00000
        7.048
        7.10224
        6.99277
        40
        IDH_ECOLI
        AAIEYAIANDRDSVTLVHK
        1.00000
        6.287
        6.30479
        6.26890
        41
        DPO1_ECOLI
        AAINAPMQGTAADIIKR
        0.99984
        5.874
        5.89720
        5.85167
        42
        SYFA_ECOLI
        AAISQASDVAALDNVR
        1.00000
        6.883
        6.88744
        6.87875
        43
        SYFA_ECOLI
        AAISQASDVAALDNVRVEYLGK
        1.00000
        6.041
        6.09900
        5.98363
        44
        MUKF_ECOLI
        AAISSC(Carbamidomethyl)ELLLSETSGTLR
        0.99984
        5.450
        5.50568
        5.39500
        45
        MSCM_ECOLI
        AAKPAQPEVVEALQSALNALEER
        0.99993
        5.256
        5.34283
        5.16930
        46
        AMPN_ECOLI
        AALEQLKGLENLSGDLYEK
        1.00000
        6.254
        6.31384
        6.19468
        47
        DBHA_ECOLI
        AALESTLAAITESLK
        1.00000
        7.303
        7.29298
        7.31293
        48
        HEM3_ECOLI
        AALPPEISLPAVGQGAVGIEC(Carbamidomethyl)R
        0.99989
        6.310
        6.33962
        6.27974
        49
        SDHA_ECOLI
        AALQISQSGQTC(Carbamidomethyl)ALLSK
        0.99991
        5.556
        5.63444
        5.47807
        50
        DHE4_ECOLI
        AANAGGVATSGLEMAQNAAR
        1.00000
        5.727
        5.79344
        5.66062
        First Page Previous PageNext Page Last PagePage/Total Pages

        Protein Quantification Table

        This plot shows the quantification information of proteinsin quantms pipeline final result

        The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.

        • Peptides_Number: The number of peptides for each protein.
        • Average Intensity: Average intensity of each protein across all conditions with NA=0 or NA ignored.
        • Protein intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of peptides.Click distribution to switch to bar plots.
        Showing 50/50 rows and 6/6 columns.
        ProteinNamePeptides_NumberAverage IntensityCT=Mixture;CN=UPS1;QY=0.25fmolCT=Mixture;CN=UPS1;QY=0.1fmolCT=Mixture;CN=UPS1;QY=0.25fmolCT=Mixture;CN=UPS1;QY=0.1fmol
        3PASE_ECOLI
        1
        5.62306
        5.64150
        5.60463
        5DNU_ECOLI
        1
        5.18693
        5.26208
        5.11178
        6PGD_ECOLI
        10
        7.42942
        7.44456
        7.41428
        6PGL_ECOLI
        2
        6.50260
        6.53307
        6.47213
        AAEB_ECOLI
        1
        6.17840
        6.21578
        6.14101
        AAS_ECOLI
        4
        6.06861
        6.06445
        6.07277
        AAT_ECOLI
        2
        7.17293
        7.19440
        7.15145
        ABGT_ECOLI
        1
        5.23376
        5.13743
        5.33010
        ACCA_ECOLI
        11
        7.75792
        7.79878
        7.71705
        ACCC_ECOLI
        12
        7.61525
        7.65242
        7.57807
        ACCD_ECOLI
        4
        6.95665
        6.96950
        6.94380
        ACEA_ECOLI
        10
        7.20604
        7.24753
        7.16455
        ACFD_ECOLI
        8
        6.82810
        6.86569
        6.79050
        ACKA_ECOLI
        10
        8.29284
        8.32125
        8.26443
        ACNA_ECOLI
        5
        6.10555
        6.17954
        6.03155
        ACNB_ECOLI
        11
        7.55688
        7.59335
        7.52042
        ACRA_ECOLI
        6
        7.49514
        7.53935
        7.45093
        ACRB_ECOLI
        6
        6.86423
        6.92424
        6.80422
        ACSA_ECOLI
        2
        5.59331
        5.55110
        5.63552
        ACUI_ECOLI
        5
        7.03398
        7.10966
        6.95830
        ACYP_ECOLI
        1
        5.61388
        5.62384
        5.60391
        ADD_ECOLI
        5
        7.28189
        7.30788
        7.25590
        ADEC_ECOLI
        1
        5.38668
        5.42067
        5.35270
        ADHE_ECOLI
        36
        8.65016
        8.68982
        8.61049
        ADHP_ECOLI
        2
        6.07901
        6.08247
        6.07556
        ADIA_ECOLI
        3
        5.91749
        5.98476
        5.85021
        ADPP_ECOLI
        2
        6.61200
        6.64355
        6.58045
        AGP_ECOLI
        3
        6.13662
        6.16680
        6.10643
        AHPC_ECOLI
        9
        8.12726
        8.15722
        8.09729
        AHPF_ECOLI
        9
        7.59355
        7.61117
        7.57594
        AHR_ECOLI
        1
        5.05767
        4.98011
        5.13523
        AK1H_ECOLI
        7
        6.48752
        6.51575
        6.45929
        AK2H_ECOLI
        4
        6.50095
        6.52980
        6.47209
        AK3_ECOLI
        5
        6.58938
        6.64211
        6.53665
        ALAA_ECOLI
        3
        6.60599
        6.63054
        6.58144
        ALAC_ECOLI
        5
        6.56726
        6.62291
        6.51161
        ALDB_ECOLI
        1
        6.04168
        6.07289
        6.01046
        ALF1_ECOLI
        2
        5.44720
        5.80606
        5.08834
        ALF_ECOLI
        10
        8.13548
        8.15468
        8.11628
        ALKH_ECOLI
        3
        6.64009
        6.71154
        6.56865
        ALR1_ECOLI
        3
        6.66391
        6.69737
        6.63045
        AMIA_ECOLI
        1
        5.80635
        5.84686
        5.76583
        AMIB_ECOLI
        2
        5.72767
        5.76208
        5.69326
        AMIC_ECOLI
        5
        5.98195
        6.06762
        5.89629
        AMID_ECOLI
        1
        4.52776
        4.69717
        4.35834
        AMN_ECOLI
        8
        6.76503
        6.78775
        6.74232
        AMPA_ECOLI
        7
        7.26489
        7.29686
        7.23293
        AMPC_ECOLI
        2
        6.11671
        6.17133
        6.06209
        AMPH_ECOLI
        2
        6.15217
        6.21212
        6.09222
        AMPN_ECOLI
        7
        7.10627
        7.13058
        7.08197
        First Page Previous PageNext Page Last PagePage/Total Pages

        nf-core/quantms Software Versions

        are collected at run time from the software output.

        Process Name Software Version
        ASSEMBLE_EMPIRICAL_LIBRARY DIA-NN 1.8.1
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.9.5
        yaml 5.4.1
        DIANNCFG sdrf-pipelines 0.0.21
        DIANNCONVERT sdrf-pipelines 0.0.21
        DIANNSUMMARY DIA-NN 1.8.1
        DIANN_PRELIMINARY_ANALYSIS DIA-NN 1.8.1
        INDIVIDUAL_FINAL_ANALYSIS DIA-NN 1.8.1
        MSSTATS bioconductor-msstats 4.2.0
        r-base 4.1.2
        SAMPLESHEET_CHECK sdrf-pipelines 0.0.21
        SDRFPARSING sdrf-pipelines 0.0.21
        THERMORAWFILEPARSER ThermoRawFileParser 1.3.4
        Workflow Nextflow 21.10.6
        nf-core/quantms 1.1dev

        nf-core/quantms Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        runName
        voluminous_thompson
        containerEngine
        docker
        launchDir
        /home/chengxin/newPR/quantms
        workDir
        /home/chengxin/newPR/quantms/work
        projectDir
        /home/chengxin/newPR/quantms
        userName
        chengxin
        profile
        test_dia,docker
        configFiles
        /home/chengxin/newPR/quantms/nextflow.config

        Input/output options

        input
        /home/chengxin/diatestdata/PXD026600/PXD026600Partial2.sdrf.tsv
        outdir
        ./results_dia

        Protein database

        database
        /home/chengxin/diatestdata/PXD026600/REF_EColi_K12_UPS1_combined.fasta

        Database search

        allowed_missed_cleavages
        1
        instrument
        N/A
        max_precursor_charge
        3
        min_peptide_length
        15
        max_peptide_length
        30
        max_mods
        2

        Modification localization

        luciphor_debug
        N/A

        PSM re-scoring (general)

        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        N/A

        Consensus ID

        consensusid_considered_top_hits
        N/A
        min_consensus_support
        N/A

        Isobaric analyzer

        select_activation
        HCD

        Protein Quantification (DDA)

        ratios
        N/A
        normalize
        N/A
        fix_peptides
        N/A

        DIA-NN

        acquisition_method
        N/A
        mass_acc_ms2
        13
        mass_acc_ms1
        7
        scan_window
        8
        min_pr_mz
        350
        max_pr_mz
        950
        min_fr_mz
        500
        max_fr_mz
        1500
        diann_normalize
        N/A

        Statistical post-processing

        contrasts
        pairwise

        Quality control

        enable_pmultiqc
        true

        Institutional config options

        config_profile_name
        Test profile for DIA
        config_profile_description
        Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.

        Max job request options

        max_cpus
        2
        max_memory
        6 GB
        max_time
        2d

        Generic options

        hostnames
        N/A